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JAL-2999 release date for 2.10.4b1 set for 27th May 2018
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
Gff3Helper.java
diff --git
a/src/jalview/io/gff/Gff3Helper.java
b/src/jalview/io/gff/Gff3Helper.java
index
8af3933
..
c7e1d7a
100644
(file)
--- a/
src/jalview/io/gff/Gff3Helper.java
+++ b/
src/jalview/io/gff/Gff3Helper.java
@@
-152,8
+152,8
@@
public class Gff3Helper extends GffHelperBase
*/
if ("-".equals(strand))
{
*/
if ("-".equals(strand))
{
- System.err
- .println("Skipping mapping from reverse complement as not yet supported");
+ System.err.println(
+ "Skipping mapping from reverse complement as not yet supported");
return null;
}
return null;
}
@@
-244,7
+244,8
@@
public class Gff3Helper extends GffHelperBase
* @return
*/
@SuppressWarnings("unused")
* @return
*/
@SuppressWarnings("unused")
- protected String findTargetId(String target, Map<String, List<String>> set)
+ protected String findTargetId(String target,
+ Map<String, List<String>> set)
{
return target;
}
{
return target;
}
@@
-275,8
+276,8
@@
public class Gff3Helper extends GffHelperBase
* @throws IOException
*/
protected SequenceFeature processProteinMatch(
* @throws IOException
*/
protected SequenceFeature processProteinMatch(
- Map<String, List<String>> set, SequenceI seq,
- String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
+ Map<String, List<String>> set, SequenceI seq, String[] gffColumns,
+ AlignmentI align, List<SequenceI> newseqs,
boolean relaxedIdMatching)
{
// This is currently tailored to InterProScan GFF output:
boolean relaxedIdMatching)
{
// This is currently tailored to InterProScan GFF output:
@@
-312,7
+313,7
@@
public class Gff3Helper extends GffHelperBase
*/
int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
SequenceFeature sf2 = new SequenceFeature(sf, 1,
*/
int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
SequenceFeature sf2 = new SequenceFeature(sf, 1,
- sequenceFeatureLength, sf.getFeatureGroup());
+ sequenceFeatureLength, sf.getFeatureGroup(), sf.getScore());
mappedSequence.addSequenceFeature(sf2);
/*
mappedSequence.addSequenceFeature(sf2);
/*
@@
-320,8
+321,8
@@
public class Gff3Helper extends GffHelperBase
* renamed with its qualified accession id; renaming has to wait until
* all sequence reference resolution is complete
*/
* renamed with its qualified accession id; renaming has to wait until
* all sequence reference resolution is complete
*/
- String accessionId = StringUtils.listToDelimitedString(
- set.get(NAME), ",");
+ String accessionId = StringUtils
+ .listToDelimitedString(set.get(NAME), ",");
if (accessionId.length() > 0)
{
String database = sf.getType(); // TODO InterProScan only??
if (accessionId.length() > 0)
{
String database = sf.getType(); // TODO InterProScan only??